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John Davey
A data scientist and software engineer with two decades of bioinformatics experience, delivering robust results efficiently to clients large and small.
Experience
Principal Bioinformatician
Remote
present - 2023
- Built Target Triage and other data mining packages, gathering and synthesising public data automatically for analysis reports to help clients select drug targets faster.
- Maintained and contributed to core code base of R, SQL and Javascript with Docker / Git / CI/CD.
- Set up and ran technical skills discussion group for Operations team to share expertise and consider policy choices.
Bioinformatics Team Leader
Fios Genomics
Remote
2023 - 2022
- Managed multiple long-running data analysis projects with large corporate clients in flexible teams of two to six analysts, including oncology clinical trials, proteomics, metabolomics and DNA/RNA sequencing. Also line managed a team of three analysts.
Senior Bioinformatician
Fios Genomics
Remote
2022 - 2021
- Delivered analysis reports for many different clients, involving machine learning models (elastic net, random forest, other regression and classification techniques) and many bioinformatics tools, based on DNA and RNA sequencing (Illumina, PacBio, Oxford Nanopore), methylation and other data sources.
Bioinformatician
Bioscience Technology Facility, Department of Biology
University of York
2021 - 2016
- Collaborated with a majority of the 70+ labs in the deparment on many kinds of data analysis projects, such as:
- Tapestry, a tool to visualise, edit and report on complete long read assemblies of small eukaryotic genomes (see end-to-end Oxford Nanopore assembly of Angomonas deanei).
- Cluster analysis of RNA-sequencing time course data with scikit-learn to identify effectors of circadian rhythms in Arabidopsis thaliana (Román et al., PNAS, 2021).
- Taught courses in Python, gene expression and basic single cell analysis.
- Organised regular bioinformatics meetings and clinics to share expertise throughout the department.
Herchel Smith Postdoctoral Fellow
Professor Chris Jiggins’s lab, Department of Zoology
University of Cambridge
2016 - 2013
- One of a team of postdoctoral researchers executing an ERC advanced grant on the causes of speciation in Heliconius butterflies. Focussed on genome structure and chromosome inversions, which required developing new techniques for genome assembly (Davey et al., 2017, Davey et al., 2016).
- Led a team of twenty to design and present an exhibit on butterfly speciation for the Royal Society Summer Science Exhibition in 2014.
Postdoctoral Bioinformatician
Professor Mark Blaxter’s lab, Institute of Evolutionary Biology
University of Edinburgh
2012 - 2008
- Developed techniques for RAD Sequencing (genotyping by sequencing), analysed RAD-Seq data sets from many different collaborators across the UK (for example, Baxter et al., 2011, Houston et al., 2012, Richards et al., 2013, Liu et al, 2013) and published several major reviews and assessments(https://doi.org/10.1038/nrg3012) of the technique (Davey et al. 2011, (Davey et al. 2013).
- Organised several UK RAD Sequencing meetings, hosting the inventors of the technique to publicise the method across the community.
Software Engineer
N/A
N/A
2004 - 2002
Worked as a tester and developer on a large C codebase with Oracle SQL database (ask for details).
Education
Ph.D., Neuroinformatics
N/A
University of Edinburgh
2008 - 2005
Thesis title: The Identification of Beta-Catenin and Other RNAs in Developing Thalamic Axons
M. Sc. in Software Engineering
N/A
University of Durham
2001
B. Sc. in Computer Science (1st class Honours)
N/A
University of Durham
1997 - 2000